Optimal growth temperature of prokaryotes correlates with class II amino acid composition

FEBS Letters ◽  
2006 ◽  
Vol 580 (6) ◽  
pp. 1672-1676 ◽  
Author(s):  
Liron Klipcan ◽  
Ilya Safro ◽  
Boris Temkin ◽  
Mark Safro
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Growth Temperature ◽  
Optimal Growth ◽  
Class Ii ◽  
Optimal Growth Temperature

scholarly journals The molecular determinants of thermoadaptation: Methanococcales as a case study

2020 ◽  
Author(s):  
M Lecocq ◽  
M Groussin ◽  
M Gouy ◽  
C Brochier-Armanet
Keyword(s):  
Amino Acid ◽  
Growth Temperature ◽  
Optimal Growth ◽  
Fine Tuning ◽  
Strongly Correlated ◽  
Optimal Growth Temperature ◽  
Archaeal Lineage ◽  
Sequence Reconstruction ◽  
Temperature Impacts

Abstract Previous reports have shown that environmental temperature impacts proteome evolution in Bacteria and Archaea. However, it is unknown whether thermoadaptation mainly occurs via the sequential accumulation of substitutions, massive horizontal gene transfers, or both. Measuring the real contribution of amino acid substitution to thermoadaptation is challenging, because of confounding environmental and genetic factors (e.g. pH, salinity, genomic G+C content) that also affect proteome evolution. Here, using Methanococcales, a major archaeal lineage, as a study model, we show that optimal growth temperature is the major factor affecting variations in amino acid frequencies of proteomes. By combining phylogenomic and ancestral sequence reconstruction approaches, we disclose a sequential substitutional scheme in which lysine plays a central role by fine tuning the pool of arginine, serine, threonine, glutamine, and asparagine, whose frequencies are strongly correlated with optimal growth temperature. Finally, we show that colonization to new thermal niches is not associated with high amounts of horizontal gene transfers. Altogether, while the acquisition of a few key proteins through horizontal gene transfer may have favoured thermoadaptation in Methanococcales, our findings support sequential amino acid substitutions as the main factor driving thermoadaptation.

scholarly journals Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

2019 ◽  
Author(s):  
Gang Li ◽  
Kersten S. Rabe ◽  
Jens Nielsen ◽  
Martin K. M. Engqvist
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Optimal Growth ◽  
Learning Model ◽  
Rapid Identification ◽  
Machine Learning Model ◽  
Subsequent Step ◽  
The Stability

AbstractEnzymes that catalyze chemical reactions at high temperatures are used for industrial biocatalysis, applications in molecular biology, and as highly evolvable starting points for protein engineering. The optimal growth temperature (OGT) of organisms is commonly used to estimate the stability of enzymes encoded in their genomes, but the number of experimentally determined OGT values are limited, particularly for ther-mophilic organisms. Here, we report on the development of a machine learning model that can accurately predict OGT for bacteria, archaea and microbial eukaryotes directly from their proteome-wide 2-mer amino acid composition. The trained model is made freely available for re-use. In a subsequent step we OGT data in combination with amino acid composition of individual enzymes to develop a second machine learning model – for prediction of enzyme catalytic temperature optima (Topt). The resulting model generates enzymeToptestimates that are far superior to using OGT alone. Finally, we predictToptfor 6.5 million enzymes, covering 4,447 enzyme classes, and make the resulting dataset available for researchers. This work enables simple and rapid identification of enzymes that are potentially functional at extreme temperatures.

Effect of maternal diet on the amino acid composition of human uterine fluid

2014 ◽  
Author(s):  
Alexandra Jayne Kermack ◽  
Ying Cheong ◽  
Nick Brook ◽  
Nick Macklon ◽  
Franchesca D Houghton
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Maternal Diet ◽  
Uterine Fluid
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